Plants produce a variety of structural and chemical defences to deter herbivores, which can covary across every scale of biological organization. Along these lines, it has been suggested that young leaves differ from old leaves in their defence strategies, but studies have largely focused on woody plants and/or chemical traits. Thus, we lack an understanding of how structural and chemical defences ontogenetically covary across a large portion of plant diversity. We investigate the range of structural and chemical defences of thistles (tribe Cardueae), which comprise herbaceous species with a wide spectrum of defensive traits. We collected structural and chemical trait data across species and leaf ages from field collections, herbarium specimens and the literature. Species' young leaves tend to produce similar suites of traits, with greater interspecific variation in older leaves. Young leaves are dominated by chemical defences, while older leaves produce a broader range of both chemical and physical defence traits. Leaf spininess is associated with a distinct chemical profile that differs from that of non-spiny species. Our study demonstrates how defence strategies can vary across the leaves of herbaceous species and their ages. Expanding such efforts will be critical to further our macroevolutionary understanding of variation in plant defences.Read the free for this article on the Journal blog.

Abstract The rapid expansion of biodiversity data presents new opportunities to understand and forecast biosphere dynamics. However, disparate and dispersed data, taxonomic and geographic inconsistencies, pervasive quality issues, and a lack of reproducable workflows hinder synthesis, introduce biases and limit accurate assessment of biodiversity trends. The Botanical Information and Ecology Network (BIEN) addresses these challenges through two core contributions: (1) an ecosystem of modular, open‐source BIEN tools for collecting, harmonizing, validating, integrating, visualizing and analysing biodiversity data, and (2) a standardized, augmented and integrated global database (BIEN db) of plant occurrences, traits and geographic ranges. BIEN tools—including the Taxonomic Name Resolution Service (TNRS), Geographic Name Resolution Service (GNRS), Geocoordinate Validation Service (GVS) and Native Species Resolver (NSR)—enable the construction of analysis‐ready data sets. Using this framework, we integrated over 284 million botanical observation records. BIEN db (current version 4.2) is so far the most extensive compilation of standardized observation records and plant traits (25,932,454 unique trait observation records) for land plants, drawn from herbaria, ecological plots, citizen science and trait databases and integrated into a unified geospatial platform. Here, we present the BIEN workflow, the database and several use cases. The BIEN workflow and database support reproducible biodiversity science at scale. BIEN provides improved and unprecedented trait coverage, new estimates of total plant species richness, geographic ranges for over 250,000 species and global maps of plant biodiversity. These tools enable researchers to integrate disparate biodiversity observation records, generate tailored data sets, resolve taxonomic and geographic ambiguities, and estimate species richness across spatial and temporal scales for conservation and forecasting applications. BIEN provides a scalable, open and reproducible informatics platform that integrates global plant biodiversity data. By linking data infrastructure with accessible tools, BIEN democratizes biodiversity science. It enhances transparency, reproducibility and analytical capacity across the research community, enabling more scientists to address a wider range of questions in ecology, evolution and biodiversity science and engage in global change biology and biodiversity forecasting. BIEN offers a robust Open Science platform to understand and respond to the biodiversity crisis.

Potential and realized climate change-driven phenological mismatches have been reported across a variety of pairwise species' interactions. However, species often engage in more than one type of temporally structured interaction - therefore, the consequences of phenological shifts must be evaluated in this context. Synthesizing data from natural history collections, community science initiatives, and remote-sensing platforms, we analyzed the phenology of the flowering of an understory spring ephemeral species, the emergence of its specialist pollinator, and the closure of the canopy above. We determined how variation in phenological responses to climate across these interacting guilds impacts the potential pollination window of the spring ephemerals. We demonstrate that phenological responses to climate change can vary greatly among the three guilds across their interacting range. The potential pollination window was predicted to undergo divergent shifts among ecoregions across the landscape in the near future, which can impact the fitness and reproductive success of both flowers and pollinators. Our study represents a first step toward integrating phenological knowledge across multiple interacting guilds. Expanding such efforts will be critical to improving our ability to predict how ecosystems, communities, and the ecological interactions therein will be impacted by global change.

Observations and collections of organisms form the basis of our understanding of Earth's biodiversity and are an indispensable resource for global change studies. Geographic information is key, serving as the link between organisms and the environments they reside in. However, the geographic information associated with these records is often inaccurate, thus limiting their efficacy for research. While some tools for identifying erroneous coordinates have been developed, a prominent but less discussed source of inaccuracies arises from the use of gridded survey systems in many regions of the world. Here we present GridDER, a tool for identifying biodiversity records that have been designated locations based on widely used grid systems. Our tool also estimates the degree of environmental heterogeneity associated with grid systems, allowing users to make informed decisions about how to use such occurrence data in their research. We show that a significant proportion (similar to 13.5%; 261 million) of records on GBIF, the largest aggregator of natural history collection data, have potentially been assigned the centroid coordinates of grid cells of varying size, and demonstrate that our tool can reliably identify such records and quantify the associated uncertainties. GridDER can serve as a tool to not only screen for gridded points, but to quantify the geographic and environmental uncertainties associated with these records, which can be used to inform models and analyses that utilize these data, including those pertaining to global change.

Biologists increasingly rely on computer code to collect and analyze their data, reinforcing the importance of published code for transparency, reproducibility, training, and a basis for further work. Here, we conduct a literature review estimating temporal trends in code sharing in ecology and evolution publications since 2010, and test for an influence of code sharing on citation rate. We find that code is rarely published (only 6% of papers), with little improvement over time. We also found there may be incentives to publish code: Publications that share code have tended to be low-impact initially, but accumulate citations faster, compensating for this deficit. Studies that additionally meet other Open Science criteria, open-access publication, or data sharing, have still higher citation rates, with publications meeting all three criteria (code sharing, data sharing, and open access publication) tending to have the most citations and highest rate of citation accumulation.

Aim: Darwin posited th at invaders similar to native species are less likely to be successful due to competitive exclusion. A key axis across which such competition occurs across angiosperms is the timing of flowering, or reproductive phenology. It has been hypothesized that temporal isolation facilitates the establishment of introduced species. However, our knowledge of how the timing of flowering may influence invasion success is lacking at broader geographic and larger taxonomic scales. To address this impasse, we investigated: (i) how flowering phenology differs between native and non-native species; (ii) whether the flowering phenology of successful invaders is distinct from native taxa; and (iii) whether invasive species tend to be more closely related to natives than other less successful, non-invasive introduced species are. Location: California, USA. Time Period: Present. Major Taxa Studied: Angiosperms. Methods: We compiled phenological data for over 6000 angiosperm species across California, a highly invaded biodiversity hotspot, from published flora. Using these data, we assessed the degree of phenological and phylogenetic similarity among native, non-invasive introduced, and invasive species. We also examined how this similarity varies with climate. Results: Both non-invasive introduced and invasive species were more phenologically and phylogenetically distant from natives than natives were from each other. However, invasive plants tend to be more similar to native species in terms of flowering phenology and phylogenetic relationships than non-invasive introduced species. Further, the degree of similarity between native and non-native species was mediated by climate, where phenological and phylogenetic similarities were greater in cooler regions. Main Conclusions: Together, our results demonstrate that both similarity and distinctiveness can facilitate plant invasions and that invaders just similar enough to the native flora are more likely to be successful.

Biotic interactions, such as plant-animal seed dispersal mutualisms, are essential for ecosystem function. Such interactions are threatened by the possible extinction of the animal partners. Using a data set that includes plant-lemur interactions across Madagascar, we studied the current state of knowledge of these interactions and their structure to determine which plant species are most at risk of losing dispersal services due to the loss of lemurs. We found substantial gaps in understanding of plant-lemur interactions; data were substantially skewed toward a few lemur species and locations. There was also a large gap in knowledge on the interactions of plants and small-bodied or nocturnal lemurs and lemurs outside a few highly studied locations. Of the recorded interactions, a significant portion occurred between lemurs and endemic plants, rather than native or introduced plants. We also found that lemur species tended to primarily consume closely related plant species. Such interaction patterns may indicate the threats to Malagasy endemic plants and highlight how lemur population loss or reductions could affect plant phylogenetic diversity. When examining the impacts of lemur extinction, losing critically endangered species left 164 plant species with no known lemur frugivore partners. Despite phylogenetic patterns in lemur diet, plants for which the only known lemur frugivore is critically endangered were not closely related. These results emphasize the need for further studies to complete our knowledge on these essential interactions and to inform conservation priorities.

Aim: Species occurrence data are valuable information that enables one to estimate geographical distributions, characterize niches and their evolution, and guide spatial conservation planning. Rapid increases in species occurrence data stem from increasing digitization and aggregation efforts, and citizen science initiatives. However, persistent quality issues in occurrence data can impact the accuracy of scientific findings, underscoring the importance of filtering erroneous occurrence records in biodiversity analyses. Innovation: We introduce an R package, occTest, that synthesizes a growing open-source ecosystem of biodiversity cleaning workflows to prepare occurrence data for different modelling applications. It offers a structured set of algorithms to identify potential problems with species occurrence records by employing a hierarchical organization of multiple tests. The workflow has a hierarchical structure organized in testPhases (i.e. cleaning vs. testing) that encompass different testBlocks grouping different testTypes (e.g. environmental outlier detection), which may use different testMethods (e.g. Rosner test, jacknife,etc.). Four different testBlocks characterize potential problems in geographic, environmental, human influence and temporal dimensions. Filtering and plotting functions are incorporated to facilitate the interpretation of tests. We provide examples with different data sources, with default and user-defined parameters. Compared to other available tools and workflows, occTest offers a comprehensive suite of integrated tests, and allows multiple methods associated with each test to explore consensus among data cleaning methods. It uniquely incorporates both coordinate accuracy analysis and environmental analysis of occurrence records. Furthermore, it provides a hierarchical structure to incorporate future tests yet to be developed. Main conclusions: occTest will help users understand the quality and quantity of data available before the start of data analysis, while also enabling users to filter data using either predefined rules or custom-built rules. As a result, occTest can better assess each record's appropriateness for its intended application.

Aim Species occurrence records are essential to understanding Earth's biodiversity and addressing global environmental issues, but do not always reflect actual locations of occurrence. Certain geographical coordinates are assigned repeatedly to thousands of observation/collection records. This may result from imperfect data management and georeferencing practices, and can greatly bias the inferred distribution of biodiversity and associated environmental conditions. Nonetheless, these 'biodiverse' coordinates are often overlooked in taxon-centric studies, as they are identifiable only in aggregate across taxa and datasets, and it is difficult to determine their true circumstance without in-depth, focused investigation. Here we assess highly recurring coordinates in biodiversity data to determine artificial hotspots of occurrences.Location Global.Taxon Land plants, birds, mammals, insects.Methods We identified highly recurring coordinates across plant, bird, insect and mammal records in the Global Biodiversity Information Facility, the largest aggregator of biodiversity data. We determined which are likely artificial hotspots by examining metadata from over 40 million records, assessing spatial distributions of associated datasets, contacting data managers and reviewing literature. These results were compiled into the Artificial Hotspot Occurrence Inventory (AHOI).Results Artificial biodiversity hotspots generally comprised geopolitical and grid centroids. The associated uncertainty ranged from several square kilometres to millions. Such artificial biodiversity hotspots were most prevalent in plant records. For instance, over 100,000 plant occurrence records were assigned the centroid coordinates of Brazil, and points that have at least 1000 associated occurrences comprised over 9 million records. In contrast, highly recurring coordinates in animal data more often reflected actual sites of observation.Main conclusions AHOI can be used to (i) improve accuracy of biodiversity assessments; (ii) estimate uncertainty associated with records from artificial hotspots and make informed decisions on whether to include them in scientific studies; and (iii) identify problems in biodiversity informatics workflows and priorities for improvement.

Biologists increasingly rely on computer code to collect and analyze their data, reinforcing the importance of published code for transparency, reproducibility, training, and a basis for further work. Here we conduct a literature review examining temporal trends in code sharing in ecology and evolution publications since 2010, and test for an influence of code sharing on citation rate. We find that there is wide room for improvement in sharing code, as scientists are overwhelmingly (95%) failing to publish their code and that there has been no significant improvement over time. We also determined that there is a significant incentive to share, as we additionally find that code sharing can considerably improve citations, particularly when combined with open-access publication.

Herbarium collections shape our understanding of Earth's flora and are crucial for addressing global change issues. Their formation, however, is not free from sociopolitical issues of immediate relevance. Despite increasing efforts addressing issues of representation and colonialism in natural history collections, herbaria have received comparatively less attention. While it has been noted that the majority of plant specimens are housed in the Global North, the extent and magnitude of this disparity have not been quantified. Here we examine the colonial legacy of botanical collections, analysing 85,621,930 specimen records and assessing survey responses from 92 herbarium collections across 39 countries. We find an inverse relationship between where plant diversity exists in nature and where it is housed in herbaria. Such disparities persist across physical and digital realms despite overt colonialism ending over half a century ago. We emphasize the need for acknowledging the colonial history of herbarium collections and implementing a more equitable global paradigm for their collection, curation and use.

Anthropogenic climate change has significantly altered the flowering times (i.e., phenology) of plants worldwide, affecting their reproduction, survival, and interactions. Recent studies utilizing herbarium specimens have uncovered significant intra- and inter-specific variation in flowering phenology and its response to changes in climate but have mostly been limited to animal-pollinated species. Thus, despite their economic and ecological importance, variation in phenological responses to climate remain largely unexplored among and within wind-pollinated dioecious species and across their sexes. Using both herbarium specimens and volunteer observations of cottonwood ( Populus ) species, we examined how phenological sensitivity to climate varies across species, their ranges, sexes, and phenophases. The timing of flowering varied significantly across and within species, as did their sensitivity to spring temperature. In particular, male flowering generally happened earlier in the season and was more sensitive to warming than female flowering. Further, the onset of flowering was more sensitive to changes in temperature than leaf out. Increased temporal gaps between male and female flowering time and between the first open flower date and leaf out date were predicted for the future under two climate change scenarios. These shifts will impact the efficacy of sexual reproduction and gene flow among species. Our study demonstrates significant inter- and intra-specific variation in phenology and its responses to environmental cues, across species’ ranges, phenophases, and sex, in wind-pollinated species. These variations need to be considered to predict accurately the effects of climate change and assess their ecological and evolutionary consequences.

SummaryUrbanization can affect the timing of plant reproduction (i.e. flowering and fruiting) and associated ecosystem processes. However, our knowledge of how plant phenology responds to urbanization and its associated environmental changes is limited.Herbaria represent an important, but underutilized source of data for investigating this question. We harnessed phenological data from herbarium specimens representing 200 plant species collected across 120 yr from the eastern US to investigate the spatiotemporal effects of urbanization on flowering and fruiting phenology and frost risk (i.e. time between the last frost date and flowering).Effects of urbanization on plant reproductive phenology varied significantly in direction and magnitude across species ranges. Increased urbanization led to earlier flowering in colder and wetter regions and delayed fruiting in regions with wetter spring conditions. Frost risk was elevated with increased urbanization in regions with colder and wetter spring conditions.Our study demonstrates that predictions of phenological change and its associated impacts must account for both climatic and human effects, which are context dependent and do not necessarily coincide. We must move beyond phenological models that only incorporate temperature variables and consider multiple environmental factors and their interactions when estimating plant phenology, especially at larger spatial and taxonomic scales.

Coevolution played a central role in shaping biodiversity. However, coevolutionary events driving reciprocal diversification between interacting partners lack empirical evidences. Examples of diversification arising from mutualisms and antagonisms at different trophic levels are scarce, which limits our understanding on how complex relationships between species arise within communities. By adopting a cophylogenetic framework, we investigated whether congruence in plant-lemur phylogenies are driven by mutualisms and antagonisms in Madagascar, where endemic species have evolved within a unique isolated biogeographical context. Although we found weak support for coevolution, this is not to say that lemurs and plants did not share evolutionary history. Weak cophylogenetic signals do not necessarily imply lack of co-diversification. Rather, our results suggest that vertebrates and plants influenced each other evolution, but in a multi-specific context where the cophylogenetic process leaded to spatio-temporal asymmetries and shifts between periods of coevolution and independent evolution, ultimately resulting in a weak, continuous and diffuse process.

Plant phenology has been shifting dramatically in response to climate change, a shift that may have significant and widespread ecological consequences. Of particular concern are tropical biomes, which represent the most biodiverse and imperiled regions of the world. However, compared to temperate floras, we know little about phenological responses of tropical plants because long-term observational datasets from the tropics are sparse. Herbarium specimens have greatly increased our phenological knowledge in temperate regions, but similar data have been underutilized in the tropics and their suitability for this purpose has not been broadly validated. Here, we compare phenological estimates derived from field observational data (i.e., plot surveys) and herbarium specimens at various spatial and taxonomic scales to determine whether specimens can provide accurate estimations of reproductive timing and its spatial variation. Here we demonstrate that phenological estimates from field observations and herbarium specimens coincide well. Fewer than 5% of the species exhibited significant differences between flowering periods inferred from field observations versus specimens regardless of spatial aggregation. In contrast to studies based on field records, herbarium specimens sampled much larger geographic and climatic ranges, as has been documented previously for temperate plants, and effectively captured phenological responses across varied environments. Herbarium specimens are verified to be a vital resource for closing the gap in our phenological knowledge of tropical systems. Tropical plant reproductive phenology inferred from herbarium records are widely congruent with field observations, suggesting that they can (and should) be used to investigate phenological variation and their associated environmental cues more broadly across tropical biomes.

Aim Addressing global environmental challenges requires access to biodiversity data across wide spatial, temporal and taxonomic scales. Availability of such data has increased exponentially recently with the proliferation of biodiversity databases. However, heterogeneous coverage, protocols, and standards have hampered integration among these databases. To stimulate the next stage of data integration, here we present a synthesis of major databases, and investigate (a) how the coverage of databases varies across taxonomy, space, and record type; (b) what degree of integration is present among databases; (c) how integration of databases can increase biodiversity knowledge; and (d) the barriers to database integration. Location Global. Time period Contemporary. Major taxa studied Plants and vertebrates. Methods We reviewed 12 established biodiversity databases that mainly focus on geographic distributions and functional traits at global scale. We synthesized information from these databases to assess the status of their integration and major knowledge gaps and barriers to full integration. We estimated how improved integration can increase the data coverage for terrestrial plants and vertebrates. Results Every database reviewed had a unique focus of data coverage. Exchanges of biodiversity information were common among databases, although not always clearly documented. Functional trait databases were more isolated than those pertaining to species distributions. Variation and potential incompatibility of taxonomic systems used by different databases posed a major barrier to data integration. We found that integration of distribution databases could lead to increased taxonomic coverage that corresponds to 23 years' advancement in data accumulation, and improvement in taxonomic coverage could be as high as 22.4% for trait databases. Main conclusions Rapid increases in biodiversity knowledge can be achieved through the integration of databases, providing the data necessary to address critical environmental challenges. Full integration across databases will require tackling the major impediments to data integration: taxonomic incompatibility, lags in data exchange, barriers to effective data synchronization, and isolation of individual initiatives.

The ecological and evolutionary processes that allow alien species to establish and dominate native communities (i.e., become invasive) have been a rich area of research. Past areas of inquiry have included identifying the traits necessary to invade a community and/or determining how phylogenetic relatedness of the introduced species with the resident community can promote invasive success. Yet despite decades of research, little consensus exists about why particular species successfully invade native communities while others do not. Here we develop a conceptual framework for why only certain introduced species become invasive: optimal differentiation to the edge of trait space (EoTS). We posit that optimal differentiation leading to successful invasion into a community requires that the multi-dimensional trait space of the introduced species exists at the edge of the multi-dimensional trait space of the native community. Species that possess traits that are too different cannot enter the community because of environmental filtering, while species that are too similar will either become integrated into the community but not take over or alternatively never establish. We apply this conceptual framework to species functional traits and discuss how both genetic processes and phylogenetic processes may also result in optimal differentiation to EoTS.

Competing phylogenetic models have been proposed to explain the success of species introduced to other communities. Here, we present a study predicting the establishment success of birds introduced to Florida, Hawaii and New Zealand using several alternative models, considering species' phylogenetic relatedness to source- and recipient-range taxa, propagule pressure and traits. We find consistent support for the predictive ability of source-region phylogenetic structure. However, we find that the effects of recipient-region phylogenetic structure vary in sign and magnitude depending on inclusion of source-region phylogenetic structure, delineation of the recipient species pool and the use of phylogenetic correction in the models. We argue that tests of alternative phylogenetic hypotheses including both source and recipient community phylogenetic structure, as well as important covariates such as propagule pressure, are likely to be critical for identifying general phylogenetic patterns in introduction success, predicting future invasions and for stimulating further exploration of the underlying mechanisms of invasibility.

The last two decades have seen growing use of phylogenetic patterns to test hypotheses predicting the success of introduced species. Nearly all of these tests have focused on hypotheses pertaining to phylogenetic relatedness between introduced species and those of the recipient community, largely neglecting hypotheses regarding phylogenetic relationships in the source region. We synthesize hypotheses regarding how phylogenetic relationships of both recipient and source regions together influence establishment success. We also detail how best to account for differences in source communities within phylogenetic frameworks of invasion. Existing studies have predominantly focused on the environmental filtering and competition‐relatedness hypotheses, which deal with relatedness to the recipient community. We discuss how these recipient–region hypotheses can be integrated with three hypotheses focused on the relatedness between an introduced species and the source community in which it originated: the evolutionary imbalance, universal tradeoff and competitive constraint hypotheses. We detail important issues that arise when testing alternative hypotheses and interpreting results. We highlight a lack of tests of synthetic phylogenetic hypotheses including both the source and recipient community phylogenetic structure, as well as important covariates such as propagule pressure. Such synthetic tests may be valuable for identifying general phylogenetic patterns in establishment success, predicting future invasions, and for stimulating further exploration of the underlying mechanisms of invasibility. We conclude with recommendations for future studies that use phylogenetic relationships to predict invasions: including source and recipient communities, using complete phylogenies and accounting for phylogenetic uncertainty, considering multiple stages of invasion and conducting analyses across spatial and phylogenetic scales where possible.